Testsuite: org.openscience.cdk.modulesuites.MstandardTests
Tests run: 567, Failures: 7, Errors: 1, Time elapsed: 18.851 sec
------------- Standard Output ---------------
graph.rebond.Bspt#addTuple does not have a test method
graph.rebond.Bspt#enumNear does not have a test method
graph.rebond.Bspt#enumSphere does not have a test method
graph.rebond.Bspt#enumHemiSphere does not have a test method
graph.rebond.Bspt#enumeration does not have a test method
graph.rebond.Bspt#dump does not have a test method
graph.BiconnectivityInspector#edgeAdded does not have a test method
graph.BiconnectivityInspector#edgeRemoved does not have a test method
graph.BiconnectivityInspector#vertexAdded does not have a test method
graph.BiconnectivityInspector#vertexRemoved does not have a test method
fingerprint.Fingerprinter#findPathes does not have a test method
fingerprint.Fingerprinter#getBondSymbol does not have a test method
fingerprint.GraphOnlyFingerprinter#getBondSymbol does not have a test method
atomtype.EStateAtomTypeMatcher#setRingSet does not have a test method
ringsearch.AllRingsFinder#findAllRings does not have a test method
ringsearch.AllRingsFinder#findAllRingsInIsolatedRingSystem does not have a test method
ringsearch.AllRingsFinder#findAllRingsInIsolatedRingSystem does not have a test method
ringsearch.SSSRFinder#findEssentialRings does not have a test method
ringsearch.SSSRFinder#findRelevantRings does not have a test method
ringsearch.SSSRFinder#findEquivalenceClasses does not have a test method
ringsearch.SSSRFinder#getSSSRWeightVector does not have a test method
ringsearch.SSSRFinder#getEquivalenceClassesSizeVector does not have a test method
ringsearch.cyclebasis.SimpleCycle#vertexList does not have a test method
ringsearch.cyclebasis.SimpleCycle#hashCode does not have a test method
ringsearch.cyclebasis.SimpleCycle#equals does not have a test method
ringsearch.cyclebasis.SimpleCycle#toString does not have a test method
ringsearch.cyclebasis.SimpleCycle#weight does not have a test method
ringsearch.cyclebasis.SimpleCycleBasis#cycles does not have a test method
ringsearch.cyclebasis.SimpleCycleBasis#weightVector does not have a test method
ringsearch.cyclebasis.SimpleCycleBasis#relevantCycles does not have a test method
ringsearch.cyclebasis.SimpleCycleBasis#essentialCycles does not have a test method
ringsearch.cyclebasis.SimpleCycleBasis#equivalenceClasses does not have a test method
ringsearch.cyclebasis.SimpleCycleBasis#getCycleEdgeIncidenceMatrix does not have a test method
ringsearch.cyclebasis.SimpleCycleBasis#getCycleEdgeIncidenceMatrix does not have a test method
ringsearch.cyclebasis.SimpleCycleBasis#constructKernelVector does not have a test method
ringsearch.cyclebasis.SimpleCycleBasis#inverseBinaryMatrix does not have a test method
ringsearch.cyclebasis.SimpleCycleBasis#edges does not have a test method
ringsearch.cyclebasis.SimpleCycleBasis did not have a TestClass annotation
ringsearch.Path#toString does not have a test method
qsar.AtomValenceTool#getValence does not have a test method
qsar.AtomValenceTool did not have a TestClass annotation
geometry.CrystalGeometryTools#fractionalToCartesian does not have a test method
geometry.CrystalGeometryTools#hasCrystalCoordinates does not have a test method
geometry.GeometryTools#get2DCenter does not have a test method
geometry.GeometryTools#get2DCenter does not have a test method
geometry.GeometryTools#get2DCenter does not have a test method
geometry.GeometryTools#get2DCenter does not have a test method
geometry.GeometryTools#get3DCenter does not have a test method
geometry.GeometryTools#translateAllPositive does not have a test method
geometry.GeometryTools#translate2D does not have a test method
geometry.GeometryTools#translate2D does not have a test method
geometry.GeometryTools#scaleMolecule does not have a test method
geometry.GeometryTools#scaleMolecule does not have a test method
geometry.GeometryTools#get2DDimension does not have a test method
geometry.GeometryTools#getMinMax does not have a test method
geometry.GeometryTools#translate2DCentreOfMassTo does not have a test method
geometry.GeometryTools#get2DCentreOfMass does not have a test method
geometry.GeometryTools#translate2DCenterTo does not have a test method
geometry.GeometryTools#get3DCentreOfMass does not have a test method
geometry.GeometryTools#getAngle does not have a test method
geometry.GeometryTools#distanceCalculator does not have a test method
geometry.GeometryTools#distanceCalculator does not have a test method
geometry.GeometryTools#getBondCoordinates does not have a test method
geometry.GeometryTools#getClosestAtom does not have a test method
geometry.GeometryTools#getClosestAtom does not have a test method
geometry.GeometryTools#getClosestBond does not have a test method
geometry.GeometryTools#getClosestBond does not have a test method
geometry.GeometryTools#sortBy2DDistance does not have a test method
geometry.GeometryTools#getScaleFactor does not have a test method
geometry.GeometryTools#getBondLengthAverage does not have a test method
geometry.GeometryTools#getLength2D does not have a test method
geometry.GeometryTools#has2DCoordinates does not have a test method
geometry.GeometryTools#has2DCoordinates does not have a test method
geometry.GeometryTools#has2DCoordinates does not have a test method
geometry.GeometryTools#has2DCoordinatesNew does not have a test method
geometry.GeometryTools#has3DCoordinates does not have a test method
geometry.GeometryTools#calculatePerpendicularUnitVector does not have a test method
geometry.GeometryTools#getNormalizationFactor does not have a test method
geometry.GeometryTools#getBestAlignmentForLabel does not have a test method
geometry.GeometryTools#getBestAlignmentForLabelXY does not have a test method
geometry.GeometryTools#findClosestInSpace does not have a test method
geometry.GeometryTools#mapAtomsOfAlignedStructures does not have a test method
geometry.GeometryTools#getBondLengthRMSD does not have a test method
geometry.GeometryTools#getAngleRMSD does not have a test method
geometry.GeometryTools#getAllAtomRMSD does not have a test method
geometry.GeometryTools#getHeavyAtomRMSD does not have a test method
geometry.GeometryTools#getBondLengthAverage3D does not have a test method
geometry.GeometryTools#rotate does not have a test method
geometry.GeometryTools#rotate does not have a test method
geometry.GeometryTools#normalize does not have a test method
geometry.GeometryTools#center does not have a test method
geometry.GeometryTools did not have a TestClass annotation
config.fragments.EStateFragments#getSmarts does not have a test method
config.fragments.EStateFragments#getNames does not have a test method
config.fragments.EStateFragments did not have a TestClass annotation
config.Symbols#getAtomicNumber does not have a test method
config.Symbols did not have a TestClass annotation
isomorphism.mcss.RMap#getId1 does not have a test method
isomorphism.mcss.RMap#getId2 does not have a test method
isomorphism.mcss.RMap#setId1 does not have a test method
isomorphism.mcss.RMap#setId2 does not have a test method
isomorphism.mcss.RMap#equals does not have a test method
isomorphism.mcss.RMap did not have a TestClass annotation
isomorphism.mcss.RGraph#getFirstGraphSize does not have a test method
isomorphism.mcss.RGraph#getSecondGraphSize does not have a test method
isomorphism.mcss.RGraph#setFirstGraphSize does not have a test method
isomorphism.mcss.RGraph#setSecondGraphSize does not have a test method
isomorphism.mcss.RGraph#getGraph does not have a test method
isomorphism.mcss.RGraph#addNode does not have a test method
isomorphism.mcss.RGraph#getSolutions does not have a test method
isomorphism.mcss.RGraph#bitSetToRMap does not have a test method
isomorphism.mcss.RGraph#setAllStructure does not have a test method
isomorphism.mcss.RGraph#setAllMap does not have a test method
isomorphism.mcss.RGraph#setMaxIteration does not have a test method
isomorphism.mcss.RGraph#projectG1 does not have a test method
isomorphism.mcss.RGraph#projectG2 does not have a test method
isomorphism.mcss.RGraph#clear does not have a test method
isomorphism.mcss.RGraph#toString does not have a test method
isomorphism.mcss.RGraph#parse does not have a test method
isomorphism.mcss.RGraph did not have a TestClass annotation
isomorphism.mcss.RNode#setExtension does not have a test method
isomorphism.mcss.RNode#getForbidden does not have a test method
isomorphism.mcss.RNode#setRMap does not have a test method
isomorphism.mcss.RNode#setForbidden does not have a test method
isomorphism.mcss.RNode#getRMap does not have a test method
isomorphism.mcss.RNode#toString does not have a test method
isomorphism.mcss.RNode#getExtension does not have a test method
isomorphism.mcss.RNode did not have a TestClass annotation
isomorphism.UniversalIsomorphismTester#project does not have a test method
isomorphism.UniversalIsomorphismTester#isSubgraph does not have a test method
isomorphism.UniversalIsomorphismTester#getSubgraphMaps does not have a test method
isomorphism.UniversalIsomorphismTester#getSubgraphAtomsMaps does not have a test method
isomorphism.UniversalIsomorphismTester#getSubgraphMap does not have a test method
isomorphism.UniversalIsomorphismTester#getOverlaps does not have a test method
isomorphism.UniversalIsomorphismTester#isIsomorph does not have a test method
isomorphism.UniversalIsomorphismTester#getIsomorphMaps does not have a test method
isomorphism.UniversalIsomorphismTester#makeAtomsMapsOfBondsMaps does not have a test method
isomorphism.UniversalIsomorphismTester#getIsomorphMap does not have a test method
isomorphism.UniversalIsomorphismTester#getIsomorphAtomsMap does not have a test method
isomorphism.UniversalIsomorphismTester#getSubgraphAtomsMap does not have a test method
isomorphism.UniversalIsomorphismTester#getBitSet does not have a test method
isomorphism.UniversalIsomorphismTester#buildRGraph does not have a test method
isomorphism.UniversalIsomorphismTester#projectList does not have a test method
isomorphism.UniversalIsomorphismTester#checkSingleAtomCases does not have a test method
isomorphism.UniversalIsomorphismTester#makeAtomsMapOfBondsMap does not have a test method
isomorphism.UniversalIsomorphismTester#search does not have a test method
isomorphism.UniversalIsomorphismTester did not have a TestClass annotation
isomorphism.AtomMappingTools#mapAtomsOfAlignedStructures does not have a test method
isomorphism.AtomMappingTools did not have a TestClass annotation
tools.IDCreator#setIDPolicy does not have a test method
tools.manipulator.RingSizeComparator#compare does not have a test method
tools.manipulator.AtomContainerManipulator#setAtomProperties does not have a test method
tools.manipulator.AtomContainerManipulator#createAllCarbonAllSingleNonAromaticBondAtomContainer does not have a test method
tools.manipulator.AtomContainerManipulator#unregisterElectronContainerListeners does not have a test method
tools.manipulator.AtomContainerManipulator#unregisterAtomListeners does not have a test method
tools.manipulator.AtomContainerManipulator#getElectronContainerArray does not have a test method
tools.manipulator.AtomContainerManipulator#getElectronContainerArray does not have a test method
tools.manipulator.AtomContainerManipulator#getMaximumBondOrder has a test method annotation 'testGetMaxBondOrder_IAtomContainer' which is not found in test class: org.openscience.cdk.tools.manipulator.AtomContainerManipulatorTest
tools.LonePairElectronChecker#allSaturated does not have a test method
tools.LonePairElectronChecker#saturate does not have a test method
tools.LonePairElectronChecker#saturate does not have a test method
tools.LonePairElectronChecker#isSaturated does not have a test method
tools.LonePairElectronChecker#isSaturated does not have a test method
tools.LonePairElectronChecker did not have a TestClass annotation
tools.HOSECodeGenerator#getHOSECode does not have a test method
tools.HOSECodeGenerator#getSpheres does not have a test method
tools.HOSECodeGenerator#getNodesInSphere does not have a test method
1: C T:C.sp3 A:false
2: C T:C.sp3 A:false
3: C T:C.sp3 A:false
4: C T:C.sp2 A:false
5: N T:N.sp2 A:false
6: N T:N.sp3 A:false
7: C T:C.sp3 A:false
8: C T:C.sp2 A:false
9: C T:C.sp2 A:false
10: O T:O.sp2 A:false
11: N T:N.amide A:false
12: C T:C.sp2 A:false
13: N T:N.sp2 A:false
14: C T:C.sp2 A:false
15: C T:C.sp2 A:false
16: C T:C.sp2 A:false
17: C T:C.sp2 A:false
18: C T:C.sp2 A:false
19: C T:C.sp2 A:false
20: C T:C.sp2 A:false
21: O T:O.sp3 A:false
22: C T:C.sp3 A:false
23: C T:C.sp3 A:false
24: S T:S.onyl A:false
25: O T:O.sp2 A:false
26: O T:O.sp2 A:false
27: N T:N.sp3 A:false
28: C T:C.sp3 A:false
29: C T:C.sp3 A:false
30: N T:N.sp3 A:false
31: C T:C.sp3 A:false
32: C T:C.sp3 A:false
33: C T:C.sp3 A:false
----
------------- ---------------- ---------------
Testcase: testCoverage(org.openscience.cdk.coverage.StandardCoverageTest): FAILED
The standard module is not fully tested! Missing number of method tests: 167 in number of classes: 25
junit.framework.AssertionFailedError: The standard module is not fully tested! Missing number of method tests: 167 in number of classes: 25
at org.openscience.cdk.coverage.CoverageAnnotationTest.runCoverageTest(CoverageAnnotationTest.java:83)
at org.openscience.cdk.coverage.StandardCoverageTest.testCoverage(StandardCoverageTest.java:42)
Testcase: testSFBug1208740(org.openscience.cdk.isomorphism.UniversalIsomorphismTesterTest): FAILED
expected:<8> but was:<9>
junit.framework.AssertionFailedError: expected:<8> but was:<9>
at org.openscience.cdk.isomorphism.UniversalIsomorphismTesterTest.testSFBug1208740(UniversalIsomorphismTesterTest.java:274)
Testcase: testBigRingSystem(org.openscience.cdk.ringsearch.AllRingsFinderTest): Caused an ERROR
Timeout for AllringsFinder exceeded
org.openscience.cdk.exception.CDKException: Timeout for AllringsFinder exceeded
at org.openscience.cdk.ringsearch.AllRingsFinder.checkTimeout(AllRingsFinder.java:386)
at org.openscience.cdk.ringsearch.AllRingsFinder.remove(AllRingsFinder.java:250)
at org.openscience.cdk.ringsearch.AllRingsFinder.doSearch(AllRingsFinder.java:184)
at org.openscience.cdk.ringsearch.AllRingsFinder.findAllRingsInIsolatedRingSystem(AllRingsFinder.java:158)
at org.openscience.cdk.ringsearch.AllRingsFinder.findAllRings(AllRingsFinder.java:120)
at org.openscience.cdk.ringsearch.AllRingsFinder.findAllRings(AllRingsFinder.java:101)
at org.openscience.cdk.ringsearch.AllRingsFinderTest.testBigRingSystem(AllRingsFinderTest.java:167)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:636)
Testcase: testClearConfig(org.openscience.cdk.tools.manipulator.AtomContainerManipulatorTest): FAILED
junit.framework.AssertionFailedError:
at org.openscience.cdk.tools.manipulator.AtomContainerManipulatorTest.testClearConfig(AtomContainerManipulatorTest.java:512)
Testcase: testListDifferences_BitSet_BitSet(org.openscience.cdk.fingerprint.FingerprinterToolTest): FAILED
expected:<29> but was:<19>
junit.framework.AssertionFailedError: expected:<29> but was:<19>
at org.openscience.cdk.fingerprint.FingerprinterToolTest.testListDifferences_BitSet_BitSet(FingerprinterToolTest.java:69)
Testcase: testBug2846213(org.openscience.cdk.graph.invariant.MorganNumbersToolsTest): FAILED
junit.framework.AssertionFailedError:
at org.openscience.cdk.graph.invariant.MorganNumbersToolsTest.testBug2846213(MorganNumbersToolsTest.java:107)
Testcase: testPolyCyclicSystem(org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetectorTest): FAILED
There should be no difference between these molecules
junit.framework.AssertionFailedError: There should be no difference between these molecules
at org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetectorTest.testPolyCyclicSystem(CDKHueckelAromaticityDetectorTest.java:768)
Testcase: testIndolizine(org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetectorTest): FAILED
Atom(11442088, S:C, H:1, AtomType(11442088, N:C.sp2, FC:0, H:SP2, NC:3, EV:4, Isotope(11442088, Element(11442088, S:C)))) should be aromatic
junit.framework.AssertionFailedError: Atom(11442088, S:C, H:1, AtomType(11442088, N:C.sp2, FC:0, H:SP2, NC:3, EV:4, Isotope(11442088, Element(11442088, S:C)))) should be aromatic
at org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetectorTest.testIndolizine(CDKHueckelAromaticityDetectorTest.java:784)